The Enigma
by WillSherJohnKhan
Summary: Her curiosity would always get her into trouble.
1. What Have I Got Myself Into?

The Kelvin Memorial Archive in London hid a secret. Above ground all appeared as you would expect. But below, out of sight of prying eyes was its true purpose – Section 31.

Section 31 was a secret branch of Starfleet. It existed outside of normal Starfleet Intelligence Agencies, dealing with external threats to the security of the Federation. Accountable to no one, they readily broke the rules when dealing with external threats, going so far as pursuing those it identified as a threat by whatever means it saw fit.

Low-level employees at Section 31 were advised that it is a special security operation, run to gather intelligence and to support the Federation in defending itself against possible attack.

It is run by Admiral Alexander Marcus, who has determined that there is a need for Section 31 to expand its realm of influence, and has set in motion plans that will see Starfleet have a darker and more menacing objective than just exploration.

Admiral Marcus watched Section 31's newest recruit as she prepared to go through the security scan.

She sub-consciously pulled at the short skirt of her blue Starfleet uniform, before running a hand through her ponytail. Then as she stepped up to the scanner Marcus could see the way her teeth worried her bottom lip.

'Good,' he thought. 'Uncertain but wanting to make a good impression.' That was what he needed, especially for the job to which he was assigning her.

He knew for one so young, she was just twenty-four, that she was already proving to be the best in her field. She was an exceptional find, not to mention hard working. That was why she had come to his attention. Her other attribute was her uncertainty. With that he was positive that he would be able to easily coerce her to do her job without misplaced concerns over conscience or morality.

As she finally made it through the scanning procedure, the admiral approached her with a smile that didn't quite reach his eyes.

"Lt Molly Hooper. Welcome to Section 31."

"Just place them on the tables over there," Molly instructed the nameless orderlies who had brought two more bodies into the morgue.

Six weeks in and she was still getting used to the fact that there were so many people who worked here who appeared not to have names.

When she had made enquires about this. She was simply told it was "a matter of security."

So she had let the matter be.

Molly was by in large hard working and not the type to 'rock the boat.' But she did possess a curious nature, and the longer she worked for Section 31, the more she had become curious to know just what she'd got herself involved with.

Her job was a good case in point. The parameters that she had understood on accepting the position had quickly changed to something else. That wasn't to say that she wasn't performing the job she'd been employed to do. She was.

It was just… Something didn't feel right.

She walked over to the newly brought in bodies. Removing the sheets that covered them, she frowned. "Definitely not right," she muttered.

Admiral Marcus had told her when she started that the corpses she would be looking at would have been experimented on.

"Experimented? In what way experimented?" she'd asked.

Marcus had waved away her concerns.

"Don't worry Lieutenant," he'd responded. "The experiments are being performed on dead bodies."

When she still looked concerned, Marcus continued.

"The bodies have been donated by various prison facilities. They are giving us prisoners who are deceased. They hope that at least in death the prisoners can make a useful contribution to society."

That had reassured Molly a little bit. At least that would mean that her work would not be of an unethical nature.

So she had agreed. And soon after the bodies started arriving.

In the six weeks since she'd come to work for Section 31 she had written countless reports on the effects to the bodies of various pathogens and agents. Many of which had not been seen since the 20th and 21st Century's.

What concerned her most was that what she was dealing with had either been eradicated due to cures being found, or the use of particular agents had been banned, for 300 years or more.

Bubonic Plague  
Small Pox  
Ebola  
Anthrax  
Mustard Gas  
HIV / AIDS

And the list went on.

The morgue had the prerequisite safety procedures to ensure that none of the contaminates could infect the population, those inside Section 31 and the general public. But even with all these safety measures, Molly was still required, for her own personal safety to wear head to foot protective clothing. And after examining every body had to go through a thorough decontamination procedure.

As time went on, Molly couldn't say in all honesty that she felt comfortable with what she was being asked to do. Nor did she understand the necessity to reintroduce highly dangerous, and in many cases lethal diseases and the like after they had been abolished for over three centuries

When she had tried to talk to Admiral Marcus about her growing concerns, she had been shocked by his response.

"Your job Lieutenant is to do what you are told. No questions asked."

"But Admiral, surely…"

And then the temperature in the room seemed to drop several degrees.

"Lt Hooper," Marcus said quietly. "You will return to your work, and do what is required of you."

He paused briefly.

"If you continue to be insubordinate, may I remind you that any cures we may have available for what you are dealing with are in very limited supply…"

It was then that Molly saw Marcus for what he really was.

With no other option she meekly retreated back to the morgue and continued to write the required reports on her findings as to the effects on the bodies that she examined.

As she began her examination of the latest corpses, she knew immediately that something was very different about them.

And her curiosity was telling her she needed to find the answer – and fast.

Even without performing any scans Molly was almost 100% certain that as much as the two corpses appeared human, they actually weren't.

She took blood samples from both, and analysed them.

The results caused as many questions as answers.

They confirmed that the bodies weren't human.

But the results also showed that there had been a mixing of genetically engineered platelets that had been added to the non-human blood. And the altered plasma may have been human.

"What is going on here?' she thought.

She walked over to her desk, sat down and began to search the file that came with the bodies.

As with all the other cadavers, information in the files was next to nothing. But just as she was about to give up, an attachment appeared.

Curious, she opened it.

It read:

Klingon Experiment – Augment Blood

Need to find if possible how to enhance Augment blood taken from Khan Noonien Singh so that it can have the capability to cause damage internally, instead of the current cosmetic affect of making Klingon's appear human.

Investigation into Eugenics Wars is proving difficult with so little information available. Fact known, a virus had been created to decimate the Augments. If this information could be confirmed and more information on the type of virus used, this could prove very useful.

Subject unwilling to give details of what he knows.

Will need to increase pressure to get a result.

Admiral A. Marcus

Molly was stunned.

Stunned, horrified, sickened.

The implications of what she'd just read didn't bare thinking about.

She got up and made her way back over to the bodies.

The Klingon bodies.

As she looked at them she realised that since she had taken the blood samples, a number of disturbing changes had taken place.

Bruises, lacerations, and the unmistakeable sign of multiple broken bones now appeared.

The Klingon's had been alive when they'd been experimented on. The bruises hinted at them being held down firmly.

And then they'd been beaten.

Then murdered.

Section 31 also contained another mystery that kept Molly awake at night.

At least in her dreams.

His name – Commander John Harrison. Section 31's weapon's expert.

He was tall, dark-haired, muscular and extremely handsome. He could have his pick of any of the female employees who were only too willing to fall at his feet.

But he ignored all of them.

A loner, he spent most of his time whether working or in private on his own. The reserved commander rarely worked or spoke with others.

In fact the only person he appeared to interact with was Admiral Marcus. Someone that even Molly could tell he clearly loathed.

Molly had only seen Commander Harrison on a few occasions. And although she felt drawn to him, there was something about him that frightened her.

Which, she reflected sadly was probably for the best. It would be unlikely that anyone like him would ever be interested in someone as plain, shy and ordinary as her.

As Molly prepared to leave for the day, her mind still focussed on what she had discovered, she spotted Commander Harrison heading for the Admiral's office.

He walked in looking determined and confident not even bothering to wait for an invitation to enter.

Admiral Marcus' office was a large, grand affair. But he liked to keep an eagle eye on those around him. So the office had been made so that two thirds of it was made up of triple glazed glass.

And this was how Molly was able to observe the two men.

And it soon became apparent that things were not going as the Commander had anticipated.

Very quickly their conversation became heated. The Admiral remained in his chair at his desk, while the Commander paced agitatedly around the room.

Though Molly couldn't hear what they said, she did catch snippets of their conversation by reading their lips.

"You promised me Admiral… If I did as you… Let them go…"

"I still need you to…"

"No! I have done all that you have asked of me… We had an agreement…"

"… If you want to see them again…"

The rest of what was said was obscured at they both turned away, continuing their argument.

Molly was about to leave when she heard the hiss of the office door as it opened.

Not wanting to be caught observing their private conversation, she stepped back into a shadowed part of the room. From where she stood though she could still see the two men.

Admiral Marcus remained in his office. He sat with a smug, self-satisfied look upon his face.

Clearly he had won that round, in a battle Molly was certain had been going on for sometime.

John Harrison stormed across and out of the room. His face was like thunder. His hands clenched with barely contained fury. The rage and hate that rolled off him was palpable.

But what remained embedded in Molly's memory was the pain, sorrow and despair that she had read in his eyes.


	2. Who Is Commander John Harrison?

The following morning Molly was finding it exceedingly difficult to concentrate on writing up her reports.

Commander John Harrison's eyes continued to haunt her.

Admiral Marcus was clearly blackmailing him.

Why?

And how?

What did he have over him?

If nothing else she now understood why the Commander was so reserved and why he kept to himself.

But how was it possible that someone as clearly brilliant as John Harrison was reported to be would allow himself to fall under the control of a snake like Admiral Marcus?

Her teeth worried her bottom lip as she tried to think of answers to all these questions.

But she couldn't.

Clearly there was something she was missing…

As it was she had other mysteries that needed solving.

And yet…

She just couldn't forget the deep sorrow of those eyes.

Letting out a resigned sigh, Molly closed down the file she'd been working on.

It was time to do a little covert sleuthing.

She was going to see if she could find out just what the admiral had on him. And then she was going to look for a possible way to help him get out of it.

Molly realised that she should probably just go and ask the man himself. But she was certain that in all likelihood he wouldn't want or need the help from a young, female, junior officer like her.

No. Better she start this on her own. If she did manage to find something useful, then she could bring it to his attention.

'Now,' she thought, frowning slightly in concentration. 'Where to begin?'

Commander John Harrison was furious, and he didn't care who knew it.

In fact he preferred it that way.

At least he would be left to work on his own, instead of having to deal with complete imbeciles.

He was not the type of man to suffer fools gladly.

'And yet,' he thought bitterly, he had undoubtedly been the biggest fool of all.

As he returned to the designs of the long-range torpedoes he was currently developing, he wondered how it could be possible for someone as superior as he could end up being tricked by someone like Alexander Marcus.

The more he thought about it, the rawer he felt.

He turned away from the plans again. He needed to decide what his cause of action was going to be.

He had to find a way to get them free.

His crew.

No. His family.

But first he had to find their location.

Then he would get them as far away from Federation space as he possibly could.

Find them yes, that was the priority.

Then find a safe way to transport them until he could find somewhere out of the way to reawaken them.

His eyes flickered back to the plans…

"Perfect," he murmured, allowing a small smile to play across his lips.

Later that night Molly began her investigation.

It wasn't unheard of for Section 31 staff to be working late. Though the building was not as busy as it was during the day, as with other organizations there was the need for shift-workers.

And those who needed to work overtime.

With Molly's workload increasing, with more and more bodies being delivered to the morgue every day, and no sign that she was going to be receiving any assistance anytime soon. It hadn't been too hard for Molly to make a case for some overtime, so that she could catch up on the backlog of administrative work.

In truth the only backlog was due to those reports that she should have been working on that morning.

But she now had the required permissions to stay back late. She'd worry about the consequences later. She may only get one shot at this. So she was determined to use that time as productively as she could.

Not certain what she was looking for or where best to look, Molly decided the best place to start was the Personnel Files.

She called up the records for Commander John Harrison.

John Harrison was just making the finishing touches to the revised plans for the long-range torpedoes, when he received a notification on his terminal of an unauthorised access to his personnel files, or at least the personnel files relating to Commander John Harrison.

The fury he had finally been able to suppress while working on his mission to rescue his crew suddenly erupted back to life.

Whoever was daring to snoop around in his files would pay, and pay dearly.

He performed a quick scan to trace for the location of the security breach.

"I have you now," he snarled, getting to his feet and leaving his office.

And made his way over to the morgue.

Molly frowned. This was all very odd. In fact she would go so far as to say that it made no sense at all.

Personnel Files, especially in an installation like Section 31 would contain a wide range of information on each employee. The idea being that the more they had on you, the easier it would be to detect if anything untoward or 'out of the ordinary', tampering of records etc were to happen.

The records that were kept went right through your working career, not just your current employer. They also included a lot of personal information relating to employees private lives. It was claimed this information was needed in the name of security.

But Commander John Harrison's records were defined by the little data there was to be found.

It was almost as if he'd just magically appeared out of nowhere a little under a year ago.

"Is that the hold Marcus has over you?" she pondered aloud.

Molly was so caught up in what she was doing she was completely unaware she was being approached from behind.

"What do you think you are doing Lieutenant?" a deep, baritone voice enquired close to her ear.

Molly jumped in fright. There had been no indication that her unauthorised access to the file had been detected.

She leapt to her feet, whirled around and collided with the impressively muscled and very solid chest of Commander John Harrison.

Stepping back she made an attempt to put some distance between them. But the Commander would have none of it, taking hold of her arms he marched her back until she was slammed up against the wall at the rear of the morgue.

"Where do you think you're going little one?" he asked.

Molly was most definitely feeling small as he towered over her.

She tilted her head back in an attempt to look him in the face, rather than be sidetracked by his magnificent physique.

But… Oh, my!

She'd never seen him close up. They worked in two completely different areas, that didn't require that they had any dealings with each other.

Molly couldn't help herself. She'd likely never get another chance. So she let her eyes wander. That jet-black hair her fingers itched to run through. The hypnotic aqua coloured eyes she could lose herself in. Those high cheekbones she wanted to trace with her fingertips. And those heavenly full lip… lips she would give anything to taste.

Molly wasn't the only one cataloguing features.

John Harrison had been surprised on finding that the one accessing his file had been this petite, plain little Lieutenant.

Though as he looked down into her big brown eyes, and observed how her teeth worried her bottom lip. He realised he may have to re-evaluate his first brief impression of her.

He suddenly frowned, annoyed with himself and where his thoughts were headed.

He mentally shook his head as he re-focussed on why it was he was here. He wanted answers and she was going to give them to him.

He moved her arms that he had held at her sides so that they were now pressed against the wall above her head. Then he pressed one of his long legs intimately between her own.

She let out a startled gasp.

"Who are you?" he demanded.

"Lieutenant Molly Hooper, Pathologist," she immediately replied.

"And why Lieutenant Molly Hooper were you looking into my personnel files?"

"I wanted to help you."

"Help me?"

She nodded.

Harrison frowned. Not the answer he was expecting. Unless…

Leaning down so that he could look her straight in the eye.

"What is Admiral Marcus up to now? It must be something in particular if he feels the need to bring in what he no doubt believes I will see as an insignificant junior officer, instead of his spy."

It took a moment for the implication of his words to sink in. But when they did she shook her head vigorously.

"No," she cried out. "You've got it wrong. I told you before I was trying to find a way to help you."

The Commander laughed, but there was no humour in it.

"And why little one would you want to help me?"

Molly was finding it difficult to think clearly with his body still pressed so close to hers.

"Could you just move back a little bit?" she asked, a little breathlessly.

"No," was the response.

Molly took a deep breath, and then wished she hadn't as her lower body rubbed against the Commander's leg, and could not conceal the shudder as her body began to beg for release.

It was then that she became aware that the Commander was not so unaffected as he outwardly appeared, if the current hard-on against her hip was anything to go by.

A tell tale blush heated her cheeks.

He watched her closely as he waited for her answer.

"I saw you the other night when you went to see the Admiral," she explained. "He's blackmailing you isn't he?"

Harrison didn't respond.

"I wanted to help you."

"Why?"

"Because Alexander Marcus isn't a very nice man," she replied. "He's up to something that doesn't feel right. When I expressed my concerns about the use of pathogens and agents that have not been around for 300 years, he implied that I would meet an unpleasant end."

Harrison frowned. Clearly the Admiral's lust for war was taking a more sinister turn.

"And then there were the findings to the most recent bodies that I examined," Molly continued. "And the attachment from Marcus in the file that I'm certain wasn't supposed to be there."

"What did you find?"

Molly looked deep into his eyes.

"You're going to think I'm crazy."

"Tell me."

"The bodies weren't human, they were Klingon. The Admiral had them injected with augmented blood from a Khan Noonien Singh," she replied.

Every muscle in Harrison's body tensed. Molly could see he was in shock.

"He took my blood," he whispered. Then realisation set in. "Used my blood," he snarled.

Molly's eyes grew wide. "But you can't be… It's not possible." She shook her head with disbelief. "How? You should be…"

He looked coldly down at her.

"What?" he asked. "Dead?"

He suddenly rammed his body deliberately against hers. Finally giving in to his primal nature as he ground his erection against her core.

Molly felt her eyes roll to the back of her head and she let out a moan.

It was music to Khan's ears.

He leaned down, brushing his lips against the shell of her sensitive ear.

"I am Khan Noonien Singh," he murmured. "Do I feel dead to you?"


	3. The Unspeakable Truth

Before Molly could offer a response Khan's lips had possession of hers, his tongue diving deep into the recesses of her mouth.

He let go of her hands so that he could bury his long fingers into her hair.

Arms now free, Molly reached up to grasp him around the neck. She rubbed herself against him and was rewarded with a desperate groan that reverberated through his body.

But as he moved his hands down her neck and shoulders, before making their way until they came to rest on the swell of her breasts, cupping them while massaging her aching nipples. Then her low keening cry brought him out of the passion-fuelled haze he had been in.

With great reluctance he released her lips. Leaning down so that his forehead rested against hers, he brought his hands up to gently hold her head as he looked directly into her eyes. He worked hard to get control over his breathing and the urges his body was demanding he fulfil.

As much as his body craved to continue, his mind was once again in control. Now was not the time.

He needed to find his crew, and get them and himself away from Marcus' clutches.

Molly watched the play of emotions Khan was battling to get under control. She saw how he finally mastered them moments before he stepped away from her.

They both stood looking at each other as frantic breaths gradually slowed.

"How… how is it possible for a man born in the twentieth century to still be living in the twenty-third?" Molly finally managed to get out.

Khan watched her closely, letting out a sigh of relief satisfied that she was not working for Marcus, and clearly had no knowledge about what the admiral had done.

"Seventy three actually."

"What?"

"There are seventy three of us. Though I was the only one Marcus reawakened."

"Reawakened you? How? Why?"

Khan reached out to her, wrapped his arm around her shoulders as he led her over to her desk, sat her down and pulled over another chair for himself.

He then began his story.

"As a child I was kidnapped off the streets where I lived."

"Were you not missed… your family…" Molly asked.

"I was an orphan, one of many on the streets of New Delhi. When we disappeared we weren't missed. There would soon be others to replace us."

"What happened to you?" she tentatively queried.

"We were experimented on," Khan replied.

He got to his feet, unable to remain still and began to pace.

"We were injected with genetically altered DNA. It made us 'better'."

"Better? In what way?"

"In all ways: strength, intellect, enhanced immunity, regenerative capabilities, better hearing, vision and an ability to adapt to any situation."

"What was the purpose of all these experiments?" Molly asked, though she had a terrible idea she knew what his answer was going to be.

"For war," Khan confirmed her fears. "We were the greatest weapons ever created. We were trained to be the ultimate soldiers. Trained to defend Earth and its people at all cost."

"What went wrong?"

"Wrong?" Khan looked at her in surprise. "Nothing went wrong."

Molly wasn't convinced. "But something happened, something changed."

He looked at her with admiration. She truly was remarkable. If only there was time for him to explore just how unique and special she was.

"We found out that we'd been implanted with neural inhibitors."

Molly frowned. "Why?"

"They didn't want us leaving the compound we had called home for fifteen years. They knew that the general population would rightly fear us. So they used the inhibitors to control us, or punish us if we tried to escape."

"What did you do?"

Khan smiled coldly. "We found out how to remove them. Then we integrated ourselves under assumed names into the world of business and government. We posed as regular humans, and we waited."

"For what?"

"For the right time to take control of the Earth," he replied calmly.

Molly felt sick, and her face went deathly pale.

"And… how… how precisely did you do that?" she stammered.

Khan stopped his relentless pacing and walked back to where Molly sat.

He crouched down beside her and took her small, delicate hands in his larger ones. He raised one hand to his mouth grazed the knuckles softly with his lips. He felt her hand tremble, and heard the catch in her breath at the contact.

Looking into her soft, brown eyes he told her honestly. "I'm afraid to say we took it by force."

"Oh God!" Molly cried, closing her eyes.

Khan continued his explanation. "We took control of the earth, splitting it up into seven territories."

He let out a sigh and Molly opened her eyes to watch him closely.

"I ruled with a firm, but fair hand. Everyone in my territory prospered. But sadly not all rulers were so generous."

"Enslavement?"

Khan nodded. "A rebellion was growing. And then the very thing made us unique became our curse."

"What do you mean?"

"Our genetically engineered DNA. Scientists discovered a virus that when introduced to our DNA caused a mutation that gradually destroyed us from the inside out."

Molly shuddered. She chewed on her bottom lip, deep in thought. 'So that was what Marcus was referring to in the attachment.'

"What happed next?" she asked.

Khan's expression became remorseful. "War," he replied sadly. "Not just against the humans, but among ourselves. Petty jealousies had arisen when some territories did better than others. It became known as The Eugenics Wars."

In a small voice Molly asked. "How many died?"

"According to the small amount of records Starfleet has pertaining to that time, over 73 million."

The figure was simply staggering.

Molly took a deep breath. "How did you escape?"

"My territories were under attack from all sides, and I knew we were not going to win. I gathered together as many of my supporters as I could and we fled. We eventually found a sleeper ship, which was how we used to travel in space. It would take so long to get anywhere in our Solar System that we used cryosleep technology, essentially freezing ourselves in sleep until we reached our destination."

Molly nodded. She remembered being taught at Starfleet Academy about how space travel worked in the twentieth and twenty-first centuries.

"We set off on the SS Botany Bay. And I hoped that when we awoke we could find somewhere where we could live in peace."

"Instead you were found by Admiral Marcus."

Khan sighed. "Yes."

"What happened?"

"He recognised the name of the ship he found drifting in space. And he recognised me. He realised he had an opportunity to exploit my intellect, and my savagery."

Molly nodded, silently encouraging him to continue.

"He decided to only reawaken me. But before doing so he had my appearance, including my voice surgically altered, so that I appeared English instead of Indian. He also had my memory wiped, so that when I woke I believed him when he told me that I was a Starfleet Officer called Commander John Harrison who worked for him at Section 31 as a weaponry expert."

"That explains the lack of data in Commander John Harrison's personnel file," Molly noted.

Khan nodded before continuing. "He told me I'd been on a secret mission to QoNo'S that had gone wrong."

"Wasn't he concerned that with your genetic enhancements that you would likely regain your memories?"

Khan smiled softly. Yes this young Lieutenant was a very intelligent one. "He knew my memories would eventually be reinstated, so he had a contingency plan worked out for when the inevitable happened."

Molly waited, though in truth she had already had an idea of what was involved in the Admiral's contingency plan.

"My crew," Khan confirmed. "When my memories returned and I realised the extent to which I had been used. I wanted to kill the only man who had been able to truly humiliate me."

"What did you do?"

"I confronted him. But he told me that if he died I would never see my crew again. He told me if I continued to help him develop new weapons and spacecraft, he promised he would reunite me with my crew once I had completed what he needed me to do for him."

"Except that he hasn't kept his end of the bargain, has he?" Molly asked.

"No," Khan replied bitterly. "The more tasks I complete, the more new ideas he comes up with."

"Do you know where your crew are being held?"

He shook his head sadly. "But I must find them."

"I could help you," Molly offered sincerely.

Khan moved his hands so that he now cradled her face and gazed deeply into her eyes.

"No little one," he replied softly. "This is my fight not yours. I don't want you involved. Alexander Marcus is a very dangerous man to cross."

Molly opened her mouth to argue with him. But Khan placed a gentle finger against her lips and shook his head, his expression stern.

Time was of the essence he needed to start putting his plan of action into motion. He could not, must not allow himself to become distracted by one sweet little Lieutenant with intelligent eyes, and …

"I must do this on my own," he stated. "You must not become involved."

Molly removed his finger from her mouth and gently placed her hand against his cheek.

"I already am involved."

Khan rested his hand over hers.

"Then for my sake do not pursue what you now know any further."

He stood up, pulling her up from her seat and enfolding her in his powerful arms. Resting his chin on the top of her head he made one final attempt to make her see sense.

"You must remain safe, Marcus is not to be trifled with. He may not be an Augment, but he can still kill you." He stepped back and looked into her upturned face. "Live for me Molly Hooper."

He then swooped down and kissed her hungrily on the lips once more, before turning and without looking back left the morgue.

Admiral Marcus was not the type of man who liked to be kept waiting. He especially didn't like it when he believed that the delays were deliberate.

He knew that the long-range torpedoes Khan had been working on were almost complete. Then he had received notification that there would be a short delay due to the need to correct a design malfunction.

Coming from anyone else this wouldn't have been an issue. What was thought could work in the design stage didn't always work when put into practice.

But when it came to the superior mind of Khan Noonien Singh, this was unheard of.

And that had made Marcus suspicious.

So he'd decided to look through the designs and any modifications Khan had made to work out what the augment was up to.

Pulling up the latest specifications on the designs, Marcus went through them meticulously. At first he didn't spot anything out of the ordinary. But looking again closely at what appeared to be only a minor alteration, and the purpose of the changes, given the one who had designed them, became clear.

"Well, well, well," Marcus murmured. "Thank you Commander. That is indeed a most excellent and ingenious idea."

Marcus then sent a transmission authorising the transfer of the torpedoes to a secure location.

Molly's head was spinning. All that she now knew made sense of what she had found in the autopsies she had performed.

But that was just a small part of what was really going on at Section 31.

Did Starfleet, and for that matter The Federation, know what was really going on here?

Did they even care?

Or did they prefer to look the other way and remain in ignorance?

Molly was truly beginning to wish that she didn't know what she knew. But her damned curiosity just wouldn't let up.

Despite Khan's warnings she knew she couldn't leave things be.

She knew he hadn't told her everything he knew. She knew he was trying to protect her, keep her safe.

But whatever it was that was going on here clearly had greater implications that simply could not be ignored.

She checked the time, took a deep breath, it was now or never. Marcus wasn't likely to still be around here this late. She left the morgue and made her way to the Admiral's office. As expected he was nowhere to be seen.

Molly was certain that whatever Marcus' true intentions were they would be found here.

She walked over to his desk and sat down. She was surprised to note that the Admiral's terminal was still on, and that he hadn't logged off.

This would make it easier for her to access any information she was trying to find, but it also made her stomach clench nervously. The Admiral was not the type of man to forget to logoff. That meant that he was still around. She wasn't going to have much time, she needed to find out what was going on and get out as quickly as possible.

What she did after that would depend on what she found.

She quickly spotted that Marcus had been checking on the progress of the new torpedoes that John – no Khan had been working on.

Skimming through his personal logs on the torpedoes, she froze when she read the transmission he had sent no more than an hour before.

"Oh my God," she whispered.

And then she felt a phaser being pressed to the back of her head.

'Idiot!' she berated herself silently.

"Lieutenant Hooper, how may I help you?"

Molly turned very slowly, determined not to show any fear. She got to her feet, and faced the Admiral, looking him in the eye.

Marcus was surprised by her move. Clearly he had underestimated her.

Molly ignored his question instead she stated. "I know Commander John Harrison is a complete fiction, and that his real name is Khan Noonien Singh."

Marcus tensed in shock. How had she come into such classified information?

"He told me."

His shock turned to anger. "So Lieutenant Hooper, you're in league with him. Traitor!"

Molly stood her ground. "There's only one traitor in this room and it isn't me."

"Don't take that tone with me Lieutenant. You don't know whom you're dealing with," he warned.

Molly kept her nerve. "I know exactly whom I'm dealing with," she replied. "A man set and determined to start a war, a dirty war with the Klingon Empire. What I don't understand is why?"

Admiral Marcus looked at her in disbelief.

"You're kidding me?" he said.

She shook her head.

"You are aware of what happened to Vulcan?"

"Of course," Molly replied. "But if I remember the events correctly, Vulcan was destroyed by a rogue Romulan from an alternate reality, not a Klingon."

"It is because of what happened on Vulcan that it has become necessary to make a pre-emptive strike against the Klingon's to neutralise any potential threat that they may pose."

Molly still couldn't follow his logic.

"Why?" she asked. "They haven't made any direct threats against The Federation."

"But the potential is there," Marcus stated. "Every time Starfleet has come into contact with the Klingon Empire they have repeatedly shown nothing but aggression."

"So what you're saying is, because the Klingon's don't want to be friends, you think this is reason enough to start a war?"

"Yes," Marcus replied unrepentant.

"And what of Khan and his crew?"

Marcus scowled at her. "What of them?"

"What happens to them once you have your war? I can't see Starfleet or The Federation being particularly pleased or comfortable with your method of enforced labour."

"Starfleet and The Federation will never know."

Molly's eyes widened with horror. "You're going to kill them, Khan and his crew."

The Admiral smiled triumphantly. "Of course," he replied. "I can't risk anyone finding out what has been going on here."

"I know what's going on," Molly bravely stated.

Marcus raised the phaser he still held in his hand. "True, which makes you a liability."

Molly turned and started to run just as Marcus fired. Her stunned body crumpled unconscious to the floor.


	4. Never Underestimate an AAugment

When Molly came to she had no idea where she was. As her eyes regained focus she realised she was sitting in the cockpit of a Starfleet Shuttle. But when she attempted to move she found she couldn't. Looking down she saw that she was restrained; her hands and feet were secured by metal restraints.

"Computer, release me," she ordered.

"Unable to comply," came the response.

"Why not?"

"Because the only one with authorization is me," came the recognizable, if somewhat disembodied voice of Admiral Marcus.

Molly turned her head, searching for and finding the small view-screen on the control panel.

"Where am I?" she demanded.

But her attempt to appear strong was undermined by the tremor in her voice.

Marcus heard it. His triumphant smirk almost splitting his face in two. "You Lieutenant Hooper are on a shuttle that has just crossed the Neutral Zone into Klingon air space."

In the shuttle the computer sounded a warning. "Shuttle is headed for the planet QoNo'S. Current heading will result in a collision with the planet. Abort. Abort."

Before Molly could open her mouth, Marcus reminded her. "All command codes for the shuttle have been redirected to my authorization only."

Molly tried desperately to free herself, but the restraints wouldn't budge.

She turned to look at Marcus, refusing to beg for her life. She was determined not to give him the satisfaction. Instead she stated. "Your fear of what may happen has driven you mad."

Marcus ignored her. "Better hope you die as the shuttle hits the planets atmosphere. Because if you should survive and the Klingon's find you, you really will wish you were dead."

He paused briefly. "And don't expect Khan to come to your rescue. No matter what he has told you, you are nothing to him."

"I never thought he would," Molly said bravely.

"He was just using you."

"As you used him."

But the view-screen had been disconnected, so he had not heard her defiant last words.

As soon as Khan discovered the torpedoes were missing, he knew there was only one person who could have taken them.

Rage and fury built up inside him, but he would not let them overwhelm him. He needed to remain clear-headed.

Since regaining his memories he had been forced to face the uncomfortable realization that he was under the power of another. And that someone was a person he regarded as totally inferior. For the one-time ruler, this had been a very bitter pill to swallow.

But he had done it.

He had very little choice.

The ultimatum had been made crystal clear. If he wanted to be reunited with his crew, he had to agree to be Marcus' pawn. Marcus wanted to start a war and Khan had the skills and knowledge he needed to achieve it.

But it soon became apparent that Marcus had, and probably never would, keep his end of the bargain.

So, desperate times called for desperate measures.

And although he had still rather frustratingly not been able to find where the Admiral kept his crew. Khan was confident in his own abilities to track them down. Once he had, he was going to need the modified torpedoes.

The now missing torpedoes…

"Lost something?" There was no mistaking the smug satisfaction in the enquiry.

Khan had of course heard Marcus when he'd entered the room, his superior hearing made sure of that. No matter how quiet the Admiral thought he was being.

He turned to face the Admiral, no longer bothering to disguise the absolute disgust he felt towards the man now standing before him.

"Where are they?" he demanded.

Marcus barely batted an eyelid. Such was the confidence he had in his hold over the Augment.

"I've taken possession of them."

"I was still working on them."

"Yes I know," Marcus responded. "The modifications you've made were… very specific."

Khan stiffened. "Meaning?"

The Admiral glared at the other man. "I may not have your superior intellect," he snapped. "But that doesn't mean I can't recognise when torpedo casings have been altered to hold cryotubes."

Khan took a step towards Marcus. "Where are they?" he asked again. Though asked quietly this time, there was no mistaking the menace behind it.

Marcus, sensing a shift in their ongoing power struggle attempted to regain control of the situation. "Your crew are safe for now," he replied.

Khan took another step closer.

Marcus looked into the Augment's eyes. They were cold, hard and emotionless. It occurred to him that threatening Khan, even if only implied was not the best way to go about things. But he was dammed if he was going to show this man any fear.

"Kill me and you'll never learn the location of your crew."

Khan paused, but only for a moment. "I will find them," he said. "With, or without your help."

Marcus realised the situation was slipping out of his control. He tried again, but his growing fear that he could no longer mask was making him desperate. "You may find your crew, but what about your little accomplice? Or was I right when I informed her you were just using her."

Khan was now only a step away from the Admiral. But he paused again as his words sunk in.

Accomplice?

He then realised Marcus was referring to Molly.

"What have you done with her?" he snarled.

Marcus, in his position of power was more used to Khan's forced capitulations to any of their arguments. But with that power now quickly fading the Admiral had never felt more vulnerable.

But then he realised that with Khan's unexpected ferocity of feeling that he was showing towards such an insignificant Lieutenant, the Admiral could not believe his good fortune. His confidence that had been dwindling now began to grow again. Khan, the great ruler had lost his heart to a little slip of a girl.

Here was an opportunity for him to regain the upper hand. He knew he was playing with fire. Khan was an undoubtedly dangerous individual. But he got an immeasurable amount of satisfaction whenever he could get a rise out of the Augment, who usually was so cool and calm. He couldn't help testing just how far he could push him.

"I wouldn't worry yourself about her," he replied. "If the shuttle she's in hasn't burnt up on entry to QoNo'S' atmosphere, then I'm sure the Klingon's will finish the job."

Marcus barely had time to realise how badly he had miscalculated the situation. Even as the words left his mouth, Khan was on him, his eyes full of unrestrained rage as he grabbed the Admiral by the head.

"You should have let me sleep," he roared as he applied pressure, and with his extraordinary strength crushed the admiral's skull.

Khan left Marcus' body where it dropped.

He went to the monitor on his desk and made quick work of accessing the movements of all Starfleet spacecraft.

It didn't take him long to find the identification of the shuttle Marcus had sent spinning uncontrollably towards the Klingon Home world.

Next he unlocked a cabinet under his desk. Opening the cabinet he removed a rectangular metallic box.

He rechecked the current position of the shuttle before entering the co-ordinates into the box.

As he felt the familiar sensation of particle beams enveloping him, he couldn't help but wonder how it was possible for Montgomery Scott, the creator of this particular device, to have not realised that the errors in his calculations, the end results that had seen him posted to Delta Vega for an indefinite period, had been due to the fact he had not considered that space was the thing that was moving.

An error he had very quickly spotted and corrected.

The cockpit of the shuttle was being inundated with various alarms. Warning of loss of stabilizers, that the shields were down and being on course to crash into the planet it was currently hurtling towards.

On top of this the shuttle's computer was doing its best to alert the only occupant of the perilous position she was currently in.

"Life support is failing."

"Evacuate! Evacuate!"

"Life support is failing."

But even though Molly wanted nothing more than to get free and escape her present predicament, she couldn't.

She had tried again, and again, and again to get lose from her restraints. But they were too strong.

She had even briefly entertained the idea that Khan might come to her rescue, her dark knight. But the closer the shuttle got to QoNo'S the less likely that possibility seemed.

After all, why should he? He barely knew her.

And as much as she hated to consider it, a nagging doubt worried her. Maybe Marcus was right. Maybe Khan had used her.

It was a sobering thought.

But as she began to lose consciousness she sincerely hoped that wasn't the case.

She could still remember the passion of his embrace and his unique taste on her tongue.

As her eyes closed for the last time she thought she glimpsed the unmistakable signs of a transporter beam. But instantly dismissed it as wishful thinking.

The metal restraints were ripped away by strong arms with a superhuman strength. Those same arms then gently lifted the unconscious Lieutenant from her seat and enfolded her against a muscular chest.

They dematerialised moments before the shuttle finally broke up into thousands of tiny pieces. All of which burnt up in the atmosphere never hitting the surface of the planet.

A war averted, with the Klingon's none the wiser.


	5. A New Beginning

For the second time Molly opened her eyes with no idea where she was. But this time she was reassured when Khan came into view.

"You little fool!" he exclaimed angrily.

Molly sighed. So not the reunion she'd been dreaming of. She struggled into a sitting position and looked around. She was on a bed in what appeared to be the Captain's quarters of a Federation Starship.

Khan was now pacing furiously around the room. "I told you not to get involved. Did you not hear me when I warned you how dangerous Marcus was?"

"I was trying to help you."

"Help me," he roared, whirling around and storming over to her. Glaring down at her he continued. "Because of you I may never find the location of my crew."

Molly bowed her head. "I'm sorry," she whispered.

As Khan looked down at her, the defeated slump of her shoulders, he felt his anger evaporate as quickly as it had erupted. Crouching down he placed his hand under her chin and lifted her head, before taking her stricken face into his hands.

"No," he replied quietly. "I'm the one that should be sorry. I have no right to take my frustration out on you."

He stood, pulling her up from the bed and into his arms. "What's done is done. If I'm going to be angry with anyone it should be myself."

"What about Admiral Marcus?"

"You don't need to worry about him anymore," he assured her. "He's dead."

When Khan offered no further explanation Molly didn't ask. She was confident that whatever the circumstances of Marcus' demise, they would have been deserved.

But as she snuggled deeper into Khan's embrace, she still couldn't help feeling some guilt. 'If she hadn't…'

"Stop it," he ordered, the order softened by the gentle brush of his lips against her worried brow.

A sigh escaped Molly's lips.

"Thank you," she said. "For rescuing me."

Khan smiled. "You are entirely welcome."

Guilt was now replaced by curiosity as she asked. "Khan, where are we exactly?"

"We're on the USS Vengeance."

"Never heard of it," she replied. But then she frowned. If she'd never heard of it before, then why did it sound familiar?

"The USS Vengeance is a Dreadnaught-class warship Marcus had me design for his war with the Klingon's," Khan explained.

Of course! Molly let out a gasp of disbelief.

"What is it?" Khan asked, becoming concerned when she didn't immediately respond. "Molly, what's wrong?"

Molly stepped out of his arms, then grabbed his hand and pulled him over to a terminal in the corner of the room.

She sat down at the terminal, using the pass codes she'd found of Marcus' personal files, she brought up the data she had discovered.

"Nothing's wrong," she reassured him, as she checked the information on the screen against the information on the ships data files. She got up from the seat, indicating to Khan that he should take her place.

As soon as he read the information, his eyes widened with surprise and delight.

In the Vengeance's weapons bay were his torpedoes. Not only that, inside the modified torpedoes were the cryotubes with his crew still safely inside them.

Khan turned to Molly. "How did you know…?" he asked completely stunned.

"I didn't. I came across the information by accident while I was trying to find out what Marcus was really up to," she replied. "I was hoping I could find something that could be used to pressure him to ensure the safe return of your crew."

When Khan turned back to the terminal, Molly was suddenly filled with self-doubt. Now that Khan had his crew, his family back. Would he want her anymore?

After all, she was just an ordinary human, while he and his crew were so much more.

"Whatever you're thinking, you're wrong."

Molly's head snapped up to find Khan standing in front of her.

He reached out a hand and gently wiped away tears she hadn't realised were streaming down her face.

Khan pulled her back into his arms, resting his cheek against the top of her head. As his fingers began to lazily slide up and down her arms, Molly shivered, but she wasn't cold.

Goosebumps appeared on her suddenly heated skin. Her nipples became painfully erect as they rubbed against her bra, and moisture pooled at the apex of her thighs.

Khan felt her reaction and he allowed himself a satisfied smile.

He eased the zip at the back of her uniform all the way down.

Molly stepped back to remove the dress, quickly followed by the black slip and then her boots.

Standing now in only her underwear she took a deep breath as she looked up at Khan. Would he like what he saw?

But she had nothing to fear. His pupils were dilated, there was a hitch in his breath, and his hands when they reached out to cup her face trembled ever so slightly.

He was in her thrall as much as she was in his.

She arched up into him when he suddenly pulled her to him and bent to capture her lips with his own.

They were both eager to continue what they had begun in the morgue. Desperate kisses were exchanged as they reacquainted themselves with each other's touch and taste.

Khan pulled away reluctantly only long enough to remove his own clothes, before easily lifting Molly and carrying her back over to the bed.

He put her down and set to work removing her bra and underwear. He then took her in his arms again, lifting her and laying her down on the bed before joining her.

Molly immediately reached out, running her hands over his chest, teasing his nipples before moving her hands up his arms and over his shoulders and around his neck.

She then pulled his head down and as her tongue entered his mouth to duel with his, her fingers buried themselves into his jet-black hair.

Khan was not idle. His hands moulded themselves over her breasts. Molly gasped when his fingers plucked at her nipples.

Lips now free, Khan planted ravenous kisses over her face, down her neck where he nibbled and sucked. He looked down at the mark left by his love bite and grinned. Unaugmented as she was Molly would wear the mark for several days,

Khan moved down her body, shoulders, breasts, naval, leaving a trail of moist kisses in his wake.

He kept going until he reached the nest of curls at the apex of her thighs. With several quick jabs of his tongue he made his way along the inner wall of her clit where he soon tasted her musky sweetness as it coated his tongue.

Then he began sucking deeply on her little nub, which caused Molly to raise her hips seeking release. Sensing she was close, he now impaled her with a firm tongue, lashing her again, and again until he was rewarded with her cries of pleasure.

Molly reached down and tried to pull him back up, but Khan had other ideas.

He lifted his head and watched her as he slid a long finger deep inside her. He smiled with satisfaction as her big brown eyes at first grew wide and then closed in pleasure. He began with a slow, even pace. But soon ramped it up, moving his finger up and down, and side to side, grazing the walls of her warm, wet cunt.

Molly lifted her hips again, grinding herself against him, she then clenching her internal muscles around his fingers as she tried desperately to find release

Khan chuckled softly. "So impatient my little one."

Molly's only response was a low drawn out moan.

Khan took pity on her, pressing harder against her clit while moving his fingers faster.

"Right… there," she cried as her thighs tensed. "Oh God, yes!" Molly screamed as she came, arching up against his hand as shudders shook her body.

This time when she made to pull him to her Khan went willingly.

He lay on his back, pulling Molly close and simply enjoyed the feel of their skin pressed together. Then he turned and burrowed his face into her long tresses that were spread across the pillows.

He smiled when he felt her hand move down his body. She clearly recovered quickly. He obligingly lay flat on his back, giving her complete access to his body.

Molly ran her hand over his chest, massaging his nipples and then moved her hand over his abs, before playfully circling his bellybutton. She continued moving down until she reached his semi-hard cock. She slid her fingers from the head to the base, then cupped his balls, giving them a gently squeeze.

Khan groaned.

Molly returned her attentions to his shaft. Her grip was firm and her rhythm steady, and it didn't take long for him to become fully hard.

But Khan needed release. He pressed her hand against his erection. "Harder," he moaned.

Molly quickened her pace, increasing the friction along his hard cock.

He raised his hips, matching her pace.

When she grazed her nails up and down his length he came hard, his hips bucking wildly while spilling his seed all over her hand.

He took a moment or two to recover before getting up from the bed and making his way over to the en-suite. He returned with a warm, wet towel that he used to clean them both with.

When Molly pulled him back onto the bed, Khan dropped the towel to the floor.

He leaned over her trekking gentle kisses over her face, neck and breasts.

But Molly would have none of this she needed him inside her right now.

Khan had no intention of disappointing her. Without further delay he entered her with one forceful thrust. He immediately stilled to savour the intense pleasure that engulfed him.

"You are so tight," he gasped against her neck. He then pulled out completely, and pushed back in, moaning with pleasure. "You were made for me."

He raised himself up so that his forearms supported him on the bed, the movement causing his lower body to press more deeply into her. He cupped her face in his hands. "I can't wait," he told her. "I need you now."

Molly smiled as she ran her hands over his shoulders and around his neck. She then raised her hips sharply causing his cock to imbed itself to the hilt. "Then take me."

Khan didn't need telling twice, he immediately increased his pace, his hips pumping frantically. The only sounds in the room now were their rapid breaths and the slap of their bodies as he continued to ram his cock into her tight, willing body.

They both cried out as they came together. As their climax washed over them they clung together unwilling to let each other go.

But Khan made sure to keep his weight off Molly as he rode out his climax as it pulsed through him. He then pulled out of her carefully before laying down and pulling her back against him.

As he thought about all that had happened since he had met the little Lieutenant, he trembled when he thought about how close he had come to losing her.

In such a short period of time she had come to mean everything to him. Initially he had tried to resist his feelings. But ultimately his heart had won over his head.

His crew was his family, but she was his life.

Drowsily Molly pulled Khan's head down so that it rested against her breast. When his lips claimed a nipple, laving it with his talented tongue, Molly clutched his head even closer to her, enjoying his ministrations.

They lay there enjoying the simple pleasure of leisurely caressing each other until they finally drifted off to sleep, deliciously sated and spent.

When Molly opened her eyes, she knew exactly where she was.

She reached out a hand to brush aside the hair that had fallen into Khan's eyes. She grinned as she continued to play with his hair. He looked less severe, less serious without his fringe slicked back.

'Have to talk to him about changing his hairstyle, at least in private,' she thought happily.

And then a sudden thought struck her.

But as she made to get out of the bed, she was pulled back. Khan loomed over her, eyes smouldering. "Where do you think you're going?"

"Your crew. We should begin reviving them."

Khan nuzzled her neck with his nose, dropping kisses on every part of her body that he could reach.

"They've been asleep for 300 years," he pointed out. "They can sleep a little longer."

Molly sighed, as his lips settled on hers. She was more than happy to agree with his logic.

Ten Months Later

Molly continued to be indispensable to Khan on so many levels that he had given up counting.

She had helped him to successfully revive all 72 members of his crew. They in turn immediately accepted her, whether due to her kind and generous nature, or because they recognised the depth of his feelings for her, it really didn't matter.

Molly had also been instrumental when it came to the best way of dealing with Starfleet.

Once they were made aware of just what lengths Admiral Marcus had been willing to go to in his attempts to start a war with the Klingon Empire, they had backed off on their threats to come after them.

They had even been more than happy for Khan to keep the Vengeance. They claimed that he was likely to need it more if he was determined to find a habitable planet to live on that was outside the Federation.

The truth was more likely that they didn't want such a potent reminder of Marcus' plans to turn Starfleet from an exploratory and peacekeeping service to a solely militarised one.

It had taken them several months, but they had finally found a planet that suited their requirements, and had even been welcomed by the local humanoid population.

For a man genetically engineered for war, Khan welcomed the opportunity of peace with open arms.

His reasons were many, but the main one was always Molly.

He reflected on their good fortune as he reclined on his side, one arm keeping his upper body upright, while with his other hand he gently explored the wonderful creation that lay between them on their bed.

Molly had been determined to have a natural childbirth. It had taken eleven long hours for their son to come into the world.

Khan looked over at her in wonder. She was exhausted, but the smile she gave him was full of wonder, delight and love.

He leaned over and kissed her tenderly on the lips.

"I love you," he whispered reverently, before lying down and gathering his wife and child in his warm embrace.

Against all the odds, across space and time, they had found each other. They had been offered a second chance, one full of love and family, and so much more.

Finis


End file.
